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Volumn 34, Issue 9, 2006, Pages 2812-2819

Yeast protein interactome topology provides framework for coordinated-functionality

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; MESSENGER RNA; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 33744822763     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl325     Document Type: Article
Times cited : (33)

References (62)
  • 2
    • 4444281384 scopus 로고    scopus 로고
    • The interactome as a tree - An attempt to visualize the protein-protein interaction network in yeast
    • Lu,H., Zhu,X., Liu,H., Skogerbo,G., Zhang,J., Zhang,Y., Cai,L., Zhao,Y., Sun,S., Xu,J. et al. (2004) The interactome as a tree - An attempt to visualize the protein-protein interaction network in yeast. Nucleic Acids Res., 32, 4804-4811.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4804-4811
    • Lu, H.1    Zhu, X.2    Liu, H.3    Skogerbo, G.4    Zhang, J.5    Zhang, Y.6    Cai, L.7    Zhao, Y.8    Sun, S.9    Xu, J.10
  • 3
    • 0035830505 scopus 로고    scopus 로고
    • A biological atlas of functional maps
    • Vidal,M. (2001) A biological atlas of functional maps. Cell, 104, 333-339.
    • (2001) Cell , vol.104 , pp. 333-339
    • Vidal, M.1
  • 4
    • 0037756723 scopus 로고    scopus 로고
    • Functional genomics and proteomics: Charting a multidimensional map of the yeast cell
    • Bader,G.D., Heilbut,A., Andrews,B., Tyers,M., Hughes,T. and Boone,C. (2003) Functional genomics and proteomics: Charting a multidimensional map of the yeast cell. Trends Cell Biol., 13, 344-356.
    • (2003) Trends Cell Biol. , vol.13 , pp. 344-356
    • Bader, G.D.1    Heilbut, A.2    Andrews, B.3    Tyers, M.4    Hughes, T.5    Boone, C.6
  • 6
    • 0035279936 scopus 로고    scopus 로고
    • Towards an understanding of complex protein networks
    • Tucker,C.L., Gera,J.F. and Uetz,P. (2001) Towards an understanding of complex protein networks. Trends Cell Biol., 11, 102-106.
    • (2001) Trends Cell Biol. , vol.11 , pp. 102-106
    • Tucker, C.L.1    Gera, J.F.2    Uetz, P.3
  • 7
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: Preparing the next generation of molecular biologists
    • Alberts,B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell,, 92, 291-294.
    • (1998) Cell , vol.92 , pp. 291-294
    • Alberts, B.1
  • 9
    • 0037306721 scopus 로고    scopus 로고
    • Protein complexes and proteome organization from yeast to man
    • Gavin,A.-C. and Superti-Fuga,G. (2003) Protein complexes and proteome organization from yeast to man. Curr. Opin. Chem. Biol., 7, 21-27.
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , pp. 21-27
    • Gavin, A.-C.1    Superti-Fuga, G.2
  • 11
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási,A.-L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nature Rev. Genet., 112, 101-114.
    • (2004) Nature Rev. Genet. , vol.112 , pp. 101-114
    • Barabási, A.-L.1    Oltvai, Z.N.2
  • 12
    • 0038718854 scopus 로고    scopus 로고
    • The structure and function of complex networks
    • Newman,M.E.J. (2003) The structure and function of complex networks. SIAM Rev., 45, 167-256.
    • (2003) SIAM Rev. , vol.45 , pp. 167-256
    • Newman, M.E.J.1
  • 13
    • 84865730611 scopus 로고
    • A set of measures of centrality based upon betweenness
    • Freeman,L. (1977) A set of measures of centrality based upon betweenness. Sociometry, 40, 35-41.
    • (1977) Sociometry , vol.40 , pp. 35-41
    • Freeman, L.1
  • 14
    • 27744469130 scopus 로고    scopus 로고
    • High betweenness proteins in the yeast protein interaction network
    • Joy,M.P., Brock,A., Ingber,D.E. and Huang,S. (2005) High betweenness proteins in the yeast protein interaction network. J. Biomed. Biotechnol., 2, 96-103.
    • (2005) J. Biomed. Biotechnol. , vol.2 , pp. 96-103
    • Joy, M.P.1    Brock, A.2    Ingber, D.E.3    Huang, S.4
  • 15
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein interaction networks
    • Hahn,M.W. and Kern,A.D. (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein interaction networks. Mol. Biol. Evol., 22, 803-806.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 17
    • 42749100809 scopus 로고    scopus 로고
    • Fast algorithm for detecting community structure in networks
    • Art. No. 066133
    • Newman,M.E.J. (2004) Fast algorithm for detecting community structure in networks. Phys. Rev., E69, Art. No. 066133.
    • (2004) Phys. Rev. , vol.E69
    • Newman, M.E.J.1
  • 18
    • 41349117788 scopus 로고    scopus 로고
    • Finding community structure in very large networks
    • art. no. 066111
    • Clauset,A., Newman,M.E.J. and Moore,C. (2004) Finding community structure in very large networks. Phys. Rev., E70, art. no. 066111.
    • (2004) Phys. Rev. , vol.E70
    • Clauset, A.1    Newman, M.E.J.2    Moore, C.3
  • 19
    • 0038294594 scopus 로고    scopus 로고
    • Communicating centrality in policy network drawings
    • Brandes,U. (2003) Communicating centrality in policy network drawings. IEEE Trans Vis. Comput. Graph., 9, 241-253.
    • (2003) IEEE Trans Vis. Comput. Graph. , vol.9 , pp. 241-253
    • Brandes, U.1
  • 20
    • 0035981014 scopus 로고    scopus 로고
    • Universal behavior of load distribution in scale-free networks
    • art. no. 278701
    • Goh,K.-I., Kahng,B. and Kim,D. (2001) Universal behavior of load distribution in scale-free networks. Phys. Rev. Lett., 87, art. no. 278701.
    • (2001) Phys. Rev. Lett. , vol.87
    • Goh, K.-I.1    Kahng, B.2    Kim, D.3
  • 23
    • 33745627943 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Nature, 403, 623-627.
    • (2001) Nature , vol.403 , pp. 623-627
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5    Sakaki, Y.6
  • 24
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 26
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 29
    • 10844254729 scopus 로고    scopus 로고
    • Shared components of protein complexes - Versatile building blocks or biochemical artefacts?
    • Krause,K., von Mering,C., Bork,P. and Dandekar,T. (2004) Shared components of protein complexes - versatile building blocks or biochemical artefacts? BioEssays, 26, 1333-1343.
    • (2004) BioEssays , vol.26 , pp. 1333-1343
    • Krause, K.1    von Mering, C.2    Bork, P.3    Dandekar, T.4
  • 30
    • 15044351289 scopus 로고    scopus 로고
    • Molecular chaperones as regulatory elements of cellular networks
    • Soti,C., Pal,C., Papp,B. and Csermely,P. (2005) Molecular chaperones as regulatory elements of cellular networks. Curr. Opin. Cell. Biol., 17, 210-215.
    • (2005) Curr. Opin. Cell. Biol. , vol.17 , pp. 210-215
    • Soti, C.1    Pal, C.2    Papp, B.3    Csermely, P.4
  • 31
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski,B., Uetz,P. and Fields,S. (2000) A network of protein-protein interactions in yeast. Nat. Biotechnol., 18, 1257-1261.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 32
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • Rives,A.W. and Galitski,T. (2003) Modular organization of cellular networks. Proc. Natl Acad. Sci. USA, 3, 1128-1133.
    • (2003) Proc. Natl Acad. Sci. USA , vol.3 , pp. 1128-1133
    • Rives, A.W.1    Galitski, T.2
  • 34
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • Vázquez,A., Flammini,A., Maritan,A. and Vespignani,A. (2003) Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol., 21, 697-700.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 697-700
    • Vázquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4
  • 35
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin,V. and Mirny,A. (2003) Protein complexes and functional modules in molecular networks. Proc. Natl Acad. Sci. USA,, 21, 12123-12128.
    • (2003) Proc. Natl Acad. Sci. USA , vol.21 , pp. 12123-12128
    • Spirin, V.1    Mirny, A.2
  • 36
    • 37649029805 scopus 로고    scopus 로고
    • Distance, dissimilarity and network community structure
    • art. no. 06101
    • Zhou,H. (2003) Distance, dissimilarity and network community structure. Phys. Rev., E67, art. no. 06101.
    • (2003) Phys. Rev. , vol.E67
    • Zhou, H.1
  • 37
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal,J.B., Enright,J.A. and Ouzounis,C.A. (2004) Detection of functional modules from protein interaction networks. Proteins, 54, 49-57.
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, J.A.2    Ouzounis, C.A.3
  • 38
    • 13244292287 scopus 로고    scopus 로고
    • Clustering proteins from interaction networks for the prediction of cellular functions
    • Art. No. 95
    • Brun,C., Herrmann,C. and Guénoche,A. (2004) Clustering proteins from interaction networks for the prediction of cellular functions. BMC Bioinformatics, 5, Art. No. 95.
    • (2004) BMC Bioinformatics , vol.5
    • Brun, C.1    Herrmann, C.2    Guénoche, A.3
  • 39
    • 25444490121 scopus 로고    scopus 로고
    • The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    • Art. no. 39
    • Dunn,R., Dudbridge,F. and Sanderson,C.M. (2005) The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics, 6, Art. no. 39.
    • (2005) BMC Bioinformatics , vol.6
    • Dunn, R.1    Dudbridge, F.2    Sanderson, C.M.3
  • 40
    • 29144442904 scopus 로고    scopus 로고
    • Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
    • Nabieva,E., Jim,K., Agarwal,A., Chazelle,B. and Singh,M. (2005) Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics, 21, I302-I310.
    • (2005) Bioinformatics , vol.21
    • Nabieva, E.1    Jim, K.2    Agarwal, A.3    Chazelle, B.4    Singh, M.5
  • 43
  • 44
    • 84930064585 scopus 로고    scopus 로고
    • Hierarchical organization in complex networks
    • Art. no. 026112
    • Ravasz,E. and Barabási,A.-L. (2003) Hierarchical organization in complex networks. Phys. Rev., E67, Art. no. 026112.
    • (2003) Phys. Rev. , vol.E67
    • Ravasz, E.1    Barabási, A.-L.2
  • 45
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • Pastor-Satorras,R., Smith,B. and Solé,R.V. (2003) Evolving protein interaction networks through gene duplication. J. Theor. Biol., 222, 199-210.
    • (2003) J. Theor. Biol. , vol.222 , pp. 199-210
    • Pastor-Satorras, R.1    Smith, B.2    Solé, R.V.3
  • 47
    • 0037423828 scopus 로고    scopus 로고
    • How the global structure of protein interaction networks evolves
    • Wagner,A. (2003) How the global structure of protein interaction networks evolves. Proc. Biol. Sci., 270, 457-466.
    • (2003) Proc. Biol. Sci. , vol.270 , pp. 457-466
    • Wagner, A.1
  • 48
    • 14744273317 scopus 로고    scopus 로고
    • Inferring network mechanisms: The Drosophila melanogaster protein interaction network
    • Middendorf,M., Ziv,E. and Wiggins,C.H. (2005) Inferring network mechanisms: The Drosophila melanogaster protein interaction network. Proc. Natl Acad. Sci. USA,, 102, 3192-3197.
    • (2005) Proc. Natl Acad. Sci. USA, , vol.102 , pp. 3192-3197
    • Middendorf, M.1    Ziv, E.2    Wiggins, C.H.3
  • 51
    • 24944565272 scopus 로고    scopus 로고
    • Some protein interaction data do not exhibit power law statistics
    • Tanaka,R., Yi,T.-M. and Doyle,J. (2005) Some protein interaction data do not exhibit power law statistics. FEBS Lett., 579, 5140-5144.
    • (2005) FEBS Lett. , vol.579 , pp. 5140-5144
    • Tanaka, R.1    Yi, T.-M.2    Doyle, J.3
  • 52
    • 4444366661 scopus 로고    scopus 로고
    • A critical and integrated view of the yeast interactome
    • Cornell,M., Paton,N.W. and Oliver,S.G. (2004) A critical and integrated view of the yeast interactome. Comp. Funct. Genom., 5, 382-402.
    • (2004) Comp. Funct. Genom. , vol.5 , pp. 382-402
    • Cornell, M.1    Paton, N.W.2    Oliver, S.G.3
  • 53
    • 26444506831 scopus 로고    scopus 로고
    • Effect of dataset selection on the topological interpretation of protein interaction networks
    • Hakes,L., Robertson,D.L. and Oliver,S.G. (2005) Effect of dataset selection on the topological interpretation of protein interaction networks. BMC Genomics, 6, 131.
    • (2005) BMC Genomics , vol.6 , pp. 131
    • Hakes, L.1    Robertson, D.L.2    Oliver, S.G.3
  • 55
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 56
    • 0036789265 scopus 로고    scopus 로고
    • Analyzing yest protein-protein interaction data obtained from different sources
    • Bader,G.D. and Hogue,C.W. (2002) Analyzing yest protein-protein interaction data obtained from different sources. Nat. Biotechnol., 20, 991-997.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 991-997
    • Bader, G.D.1    Hogue, C.W.2
  • 57
    • 0036899363 scopus 로고    scopus 로고
    • The third dimension for protein interactions and complexes
    • Aloy,P. and Russell,R.B. (2002) The third dimension for protein interactions and complexes. Trends Biochem. Sci., 27, 633-638.
    • (2002) Trends Biochem. Sci. , vol.27 , pp. 633-638
    • Aloy, P.1    Russell, R.B.2
  • 58
    • 0036805329 scopus 로고    scopus 로고
    • Bridging structural biology and genomics: Assessing protein interaction data with known complexes
    • Edwards,A.M., Kus,B., Jansen,R., Greenbaum,D., Greenblatl,J. and Gerstein,M. (2002) Bridging structural biology and genomics: Assessing protein interaction data with known complexes. Trends Genet., 18, 529-536.
    • (2002) Trends Genet. , vol.18 , pp. 529-536
    • Edwards, A.M.1    Kus, B.2    Jansen, R.3    Greenbaum, D.4    Greenblatl, J.5    Gerstein, M.6
  • 59
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • Lichtenberg,U., Jensen,L.J., Brunak,S. and Bork,P. (2005) Dynamic complex formation during the yeast cell cycle. Science, 307, 724-727.
    • (2005) Science , vol.307 , pp. 724-727
    • Lichtenberg, U.1    Jensen, L.J.2    Brunak, S.3    Bork, P.4
  • 61
    • 0037012880 scopus 로고    scopus 로고
    • Specificity and stability in topology of protein networks
    • Maslov,S. and Sneppen,K. (2002) Specificity and stability in topology of protein networks. Science, 296, 910-913.
    • (2002) Science , vol.296 , pp. 910-913
    • Maslov, S.1    Sneppen, K.2


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